We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)
how many FTICR reps per treatment type?
| SampleAssignment | reps |
|---|---|
| 50-drought-groundw-control-Intact | 2 |
| 50-drought-precip-C-Intact | 2 |
| 1.5-drought-groundw-C-Homogenized | 3 |
| 1.5-drought-groundw-C-Intact | 3 |
| 1.5-drought-groundw-control-Homogenized | 3 |
| 1.5-drought-groundw-N-Intact | 3 |
| 1.5-drought-precip-C-Homogenized | 3 |
| 1.5-drought-precip-N-Homogenized | 3 |
| 1.5-fm-precip-C-Intact | 3 |
| 1.5-fm-precip-N-Homogenized | 3 |
| 50-drought-groundw-control-Homogenized | 3 |
| 50-drought-groundw-N-Intact | 3 |
| 50-drought-precip-control-Homogenized | 3 |
| 50-fm-groundw-control-Intact | 3 |
| 50-fm-groundw-N-Homogenized | 3 |
| 50-fm-precip-control-Homogenized | 3 |
| 50-fm-precip-N-Homogenized | 3 |
| 1.5-drought-groundw-control-Intact | 4 |
| 1.5-drought-groundw-N-Homogenized | 4 |
| 1.5-drought-precip-C-Intact | 4 |
| 1.5-drought-precip-control-Homogenized | 4 |
| 1.5-drought-precip-control-Intact | 4 |
| 1.5-drought-precip-N-Intact | 4 |
| 1.5-fm-groundw-C-Homogenized | 4 |
| 1.5-fm-groundw-C-Intact | 4 |
| 1.5-fm-groundw-control-Homogenized | 4 |
| 1.5-fm-groundw-control-Intact | 4 |
| 1.5-fm-groundw-N-Homogenized | 4 |
| 1.5-fm-groundw-N-Intact | 4 |
| 1.5-fm-precip-C-Homogenized | 4 |
| 1.5-fm-precip-control-Homogenized | 4 |
| 1.5-fm-precip-control-Intact | 4 |
| 1.5-fm-precip-N-Intact | 4 |
| 50-drought-groundw-C-Homogenized | 4 |
| 50-drought-groundw-C-Intact | 4 |
| 50-drought-groundw-N-Homogenized | 4 |
| 50-drought-precip-C-Homogenized | 4 |
| 50-drought-precip-control-Intact | 4 |
| 50-drought-precip-N-Homogenized | 4 |
| 50-drought-precip-N-Intact | 4 |
| 50-fm-groundw-C-Homogenized | 4 |
| 50-fm-groundw-C-Intact | 4 |
| 50-fm-groundw-control-Homogenized | 4 |
| 50-fm-groundw-N-Intact | 4 |
| 50-fm-precip-C-Homogenized | 4 |
| 50-fm-precip-C-Intact | 4 |
| 50-fm-precip-control-Intact | 4 |
| 50-fm-precip-N-Intact | 4 |
so we select formulae seen in at least 2 reps per treatment type
unique to each amendment, in each incubation type
complex:simple compounds
tables – total peaks
| Homogenization | Moisture | Wetting | 1.5-control | 1.5-C | 1.5-N | 50-control | 50-C | 50-N |
|---|---|---|---|---|---|---|---|---|
| Intact | drought | groundw | 736 ± 180 | 1598 ± 180 | 913 ± 381 | 884 ± 0 | 2155 ± 663 | 802 ± 70 |
| Intact | drought | precip | 1008 ± 274 | 1857 ± 208 | 1326 ± 49 | 1768 ± 194 | 2823 ± 0 | 1567 ± 129 |
| Intact | fm | groundw | 915 ± 124 | 698 ± 34 | 848 ± 196 | 1144 ± 273 | 1064 ± 137 | 1036 ± 201 |
| Intact | fm | precip | 596 ± 89 | 637 ± 61 | 497 ± 80 | 1181 ± 276 | 3149 ± 272 | 1423 ± 47 |
| Homogenized | drought | groundw | 2411 ± 136 | 1863 ± 245 | 1394 ± 221 | 2149 ± 205 | 3294 ± 290 | 992 ± 227 |
| Homogenized | drought | precip | 1121 ± 391 | 1089 ± 109 | 1227 ± 151 | 1261 ± 173 | 1576 ± 701 | 1829 ± 584 |
| Homogenized | fm | groundw | 933 ± 134 | 899 ± 176 | 490 ± 47 | 2475 ± 455 | 1408 ± 175 | 568 ± 119 |
| Homogenized | fm | precip | 1475 ± 209 | 609 ± 162 | 804 ± 129 | 2208 ± 141 | 3689 ± 339 | 844 ± 255 |
tables – complex peaks
| Homogenization | Moisture | Wetting | 1.5-control | 1.5-C | 1.5-N | 50-control | 50-C | 50-N |
|---|---|---|---|---|---|---|---|---|
| Intact | drought | groundw | 520 ± 143 | 1159 ± 181 | 583 ± 241 | 778 ± 0 | 1609 ± 507 | 594 ± 61 |
| Intact | drought | precip | 733 ± 204 | 1220 ± 136 | 977 ± 25 | 1469 ± 158 | 2109 ± 0 | 1148 ± 87 |
| Intact | fm | groundw | 590 ± 93 | 431 ± 16 | 442 ± 81 | 894 ± 233 | 689 ± 79 | 747 ± 166 |
| Intact | fm | precip | 374 ± 64 | 439 ± 51 | 345 ± 62 | 905 ± 207 | 2341 ± 175 | 1039 ± 43 |
| Homogenized | drought | groundw | 2175 ± 121 | 1535 ± 227 | 1030 ± 187 | 1767 ± 215 | 2818 ± 233 | 774 ± 204 |
| Homogenized | drought | precip | 889 ± 317 | 825 ± 90 | 978 ± 133 | 1045 ± 162 | 1396 ± 667 | 1488 ± 506 |
| Homogenized | fm | groundw | 677 ± 94 | 557 ± 120 | 331 ± 32 | 2094 ± 453 | 1065 ± 178 | 425 ± 79 |
| Homogenized | fm | precip | 1007 ± 100 | 379 ± 107 | 557 ± 106 | 1605 ± 95 | 3229 ± 285 | 687 ± 229 |
overall
#>
#> Call:
#> adonis(formula = relabund_wide %>% select(aliphatic:condensed_arom) ~ (Amendments + Moisture + Wetting + Suction + Homogenization)^3, data = relabund_wide)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.14437 0.07219 7.811 0.04766 0.001 ***
#> Moisture 1 0.21505 0.21505 23.270 0.07099 0.001 ***
#> Wetting 1 0.00916 0.00916 0.991 0.00302 0.368
#> Suction 1 0.38447 0.38447 41.602 0.12691 0.001 ***
#> Homogenization 1 0.17475 0.17475 18.909 0.05768 0.001 ***
#> Amendments:Moisture 2 0.04268 0.02134 2.309 0.01409 0.052 .
#> Amendments:Wetting 2 0.05754 0.02877 3.113 0.01899 0.017 *
#> Amendments:Suction 2 0.02715 0.01357 1.469 0.00896 0.191
#> Amendments:Homogenization 2 0.13898 0.06949 7.519 0.04588 0.001 ***
#> Moisture:Wetting 1 0.01834 0.01834 1.985 0.00606 0.159
#> Moisture:Suction 1 0.05683 0.05683 6.149 0.01876 0.004 **
#> Moisture:Homogenization 1 0.00560 0.00560 0.606 0.00185 0.586
#> Wetting:Suction 1 0.04302 0.04302 4.655 0.01420 0.015 *
#> Wetting:Homogenization 1 0.05849 0.05849 6.329 0.01931 0.005 **
#> Suction:Homogenization 1 0.02368 0.02368 2.562 0.00782 0.073 .
#> Amendments:Moisture:Wetting 2 0.08926 0.04463 4.829 0.02946 0.001 ***
#> Amendments:Moisture:Suction 2 0.03187 0.01593 1.724 0.01052 0.145
#> Amendments:Moisture:Homogenization 2 0.04422 0.02211 2.392 0.01460 0.058 .
#> Amendments:Wetting:Suction 2 0.03512 0.01756 1.900 0.01159 0.096 .
#> Amendments:Wetting:Homogenization 2 0.02055 0.01027 1.112 0.00678 0.347
#> Amendments:Suction:Homogenization 2 0.08361 0.04181 4.524 0.02760 0.004 **
#> Moisture:Wetting:Suction 1 0.02044 0.02044 2.212 0.00675 0.124
#> Moisture:Wetting:Homogenization 1 0.00995 0.00995 1.077 0.00328 0.329
#> Moisture:Suction:Homogenization 1 0.02605 0.02605 2.819 0.00860 0.079 .
#> Wetting:Suction:Homogenization 1 0.01140 0.01140 1.233 0.00376 0.294
#> Residuals 136 1.25687 0.00924 0.41488
#> Total 172 3.02945 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
PERMANOVA for treatments
1.5 kPa intact cores
#>
#> Call:
#> adonis(formula = intact_1_5 %>% select(aliphatic:condensed_arom) ~ Amendments * Moisture * Wetting, data = intact_1_5)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.00603 0.003014 0.4995 0.01288 0.754
#> Moisture 1 0.07530 0.075298 12.4784 0.16088 0.001 ***
#> Wetting 1 0.05498 0.054976 9.1107 0.11746 0.001 ***
#> Amendments:Moisture 2 0.02583 0.012913 2.1399 0.05518 0.079 .
#> Amendments:Wetting 2 0.04222 0.021109 3.4981 0.09020 0.017 *
#> Moisture:Wetting 1 0.01142 0.011423 1.8931 0.02441 0.136
#> Amendments:Moisture:Wetting 2 0.05315 0.026576 4.4042 0.11356 0.006 **
#> Residuals 33 0.19913 0.006034 0.42545
#> Total 44 0.46805 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
50 kPa intact cores
#>
#> Call:
#> adonis(formula = intact_50 %>% select(aliphatic:condensed_arom) ~ Amendments * Moisture * Wetting, data = intact_50)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.08850 0.044252 5.8702 0.19694 0.001 ***
#> Moisture 1 0.01117 0.011168 1.4815 0.02485 0.237
#> Wetting 1 0.01314 0.013136 1.7426 0.02923 0.181
#> Amendments:Moisture 2 0.03599 0.017997 2.3875 0.08010 0.058 .
#> Amendments:Wetting 2 0.02278 0.011392 1.5112 0.05070 0.222
#> Moisture:Wetting 1 0.02859 0.028587 3.7923 0.06361 0.029 *
#> Amendments:Moisture:Wetting 2 0.02308 0.011538 1.5305 0.05135 0.225
#> Residuals 30 0.22615 0.007538 0.50323
#> Total 41 0.44940 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1.5 kPa homogenized cores
#>
#> Call:
#> adonis(formula = homo_1_5 %>% select(aliphatic:condensed_arom) ~ Amendments * Moisture * Wetting, data = homo_1_5)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.11805 0.059026 7.9299 0.16791 0.001 ***
#> Moisture 1 0.20467 0.204672 27.4967 0.29111 0.001 ***
#> Wetting 1 0.01808 0.018077 2.4286 0.02571 0.078 .
#> Amendments:Moisture 2 0.02850 0.014249 1.9143 0.04053 0.112
#> Amendments:Wetting 2 0.03984 0.019918 2.6758 0.05666 0.046 *
#> Moisture:Wetting 1 0.01283 0.012831 1.7238 0.01825 0.164
#> Amendments:Moisture:Wetting 2 0.05037 0.025186 3.3836 0.07164 0.021 *
#> Residuals 31 0.23075 0.007443 0.32819
#> Total 42 0.70308 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
50 kPa homogenized cores
#>
#> Call:
#> adonis(formula = homo_50 %>% select(aliphatic:condensed_arom) ~ Amendments * Moisture * Wetting, data = homo_50)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.19013 0.095065 6.7194 0.22768 0.001 ***
#> Moisture 1 0.00599 0.005993 0.4236 0.00718 0.670
#> Wetting 1 0.03243 0.032430 2.2922 0.03884 0.128
#> Amendments:Moisture 2 0.07244 0.036221 2.5602 0.08675 0.047 *
#> Amendments:Wetting 2 0.03066 0.015328 1.0835 0.03671 0.401
#> Moisture:Wetting 1 0.00933 0.009327 0.6593 0.01117 0.534
#> Amendments:Moisture:Wetting 2 0.05551 0.027754 1.9617 0.06647 0.099 .
#> Residuals 31 0.43858 0.014148 0.52520
#> Total 42 0.83506 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
individual cores
Date run: 2020-08-11
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#>
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] patchwork_1.0.1 visNetwork_2.0.9 vegan_2.5-6 lattice_0.20-41 permute_0.9-5 rmarkdown_2.3
#> [7] drake_7.12.4 ggbiplot_0.55 PNWColors_0.1.0 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1
#> [13] purrr_0.3.4 readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0
#> [19] here_0.1
#>
#> loaded via a namespace (and not attached):
#> [1] httr_1.4.2 jsonlite_1.7.0 splines_4.0.2 modelr_0.1.8 assertthat_0.2.1 highr_0.8
#> [7] base64url_1.4 blob_1.2.1 cellranger_1.1.0 yaml_2.2.1 progress_1.2.2 pillar_1.4.6
#> [13] backports_1.1.8 glue_1.4.1 digest_0.6.25 rvest_0.3.6 colorspace_1.4-1 htmltools_0.5.0
#> [19] Matrix_1.2-18 plyr_1.8.6 pkgconfig_2.0.3 broom_0.7.0 haven_2.3.1 scales_1.1.1
#> [25] mgcv_1.8-31 txtq_0.2.3 generics_0.0.2 farver_2.0.3 ellipsis_0.3.1 withr_2.2.0
#> [31] cli_2.0.2 magrittr_1.5 crayon_1.3.4 readxl_1.3.1 evaluate_0.14 storr_1.2.1
#> [37] fs_1.5.0 fansi_0.4.1 nlme_3.1-148 MASS_7.3-51.6 xml2_1.3.2 tools_4.0.2
#> [43] prettyunits_1.1.1 hms_0.5.3 lifecycle_0.2.0 munsell_0.5.0 reprex_0.3.0 cluster_2.1.0
#> [49] compiler_4.0.2 rlang_0.4.7 grid_4.0.2 rstudioapi_0.11 htmlwidgets_1.5.1 igraph_1.2.5
#> [55] labeling_0.3 gtable_0.3.0 DBI_1.1.0 R6_2.4.1 lubridate_1.7.9 knitr_1.29
#> [61] utf8_1.1.4 filelock_1.0.2 rprojroot_1.3-2 stringi_1.4.6 parallel_4.0.2 Rcpp_1.0.5
#> [67] vctrs_0.3.2 dbplyr_1.4.4 tidyselect_1.1.0 xfun_0.16